Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

Recon all clinical with multiple input scans
by Lieshout, P.B. van (Pauline) 13 Nov '23

13 Nov '23

External Email - Use Caution Dear sir/madam, I have been trying out the new recon-all-clinical algorithm. In the FreeSurferWiki on recon-all-clinical, it is not specified if I can add multiple scans (T1, FLAIR and T2, for instance) of the same individual in the recon-all-clinical command, similar to the old recon-all command. Is this possible in your new algorithm? Thanks in advance, Best, Pauline van Lieshout ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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buffer overflow detected in mris_expand
by Amanda Rodrigue 13 Nov '23

13 Nov '23

External Email - Use Caution Hello, I am running some freesurfer processes (freesurfer-linux-centos7_x86_64-7.3.2-20220804-6354275) via fmriprep 23.1.3 (singularity container version) and I'm getting the error below when running the mris_expand command. Below is the output from frmiprep but it's clear it's a freesurfer-specific error (I've highlighted the freesurfer command, output, and error in red). There was another post with the buffer overflow detected error (different command though) and it did not have a posted solution. Node: _midthickness0 Working directory: /lab-share/Psych-Glahn-e2/Public/neuro/bids/epicenter/scripts/fmriprep/work/fmriprep_23_1_wf/single_subject_10412_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0 Node inputs: args = <undefined> distance = 0.5 dt = <undefined> environ = {'SUBJECTS_DIR': '/opt/freesurfer/subjects'} graymid = <undefined> in_file = /lab-share/Psych-Glahn-e2/Public/neuro/bids/epicenter/temp/_epo/derivatives/fmriprep23_1_3/sourcedata/freesurfer/sub-10412/surf/rh.white nsurfaces = <undefined> out_name = midthickness pial = <undefined> smooth_averages = <undefined> sphere = sphere spring = <undefined> subjects_dir = /opt/freesurfer/subjects thickness = True thickness_name = <undefined> write_iterations = <undefined> Traceback (most recent call last): File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node result["result"] = node.run(updatehash=updatehash) File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run result = self._run_interface(execute=True) File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface return self._run_command(execute) File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command raise NodeExecutionError(msg) nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node _midthickness0. Cmdline: mris_expand -pial /lab-share/Psych-Glahn-e2/Public/neuro/bids/epicenter/scripts/fmriprep/work/fmriprep_23_1_wf/single_subject_10412_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.pial -thickness -thickness_name /lab-share/Psych-Glahn-e2/Public/neuro/bids/epicenter/scripts/fmriprep/work/fmriprep_23_1_wf/single_subject_10412_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.thickness /lab-share/Psych-Glahn-e2/Public/neuro/bids/epicenter/scripts/fmriprep/work/fmriprep_23_1_wf/single_subject_10412_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.white 0.5 /lab-share/Psych-Glahn-e2/Public/neuro/bids/epicenter/scripts/fmriprep/work/fmriprep_23_1_wf/single_subject_10412_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.midthickness Stdout: reading pial surface from /lab-share/Psych-Glahn-e2/Public/neuro/bids/epicenter/scripts/fmriprep/work/fmriprep_23_1_wf/single_subject_10412_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.pial using distance as a % of thickness using thickness file /lab-share/Psych-Glahn-e2/Public/neuro/bids/epicenter/scripts/fmriprep/work/fmriprep_23_1_wf/single_subject_10412_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.thickness expanding surface /lab-share/Psych-Glahn-e2/Public/neuro/bids/epicenter/scripts/fmriprep/work/fmriprep_23_1_wf/single_subject_10412_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.white by 50.0% of thickness and writing it to /lab-share/Psych-Glahn-e2/Public/neuro/bids/epicenter/scripts/fmriprep/work/fmriprep_23_1_wf/single_subject_10412_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.midthickness reading thickness... Stderr: *** buffer overflow detected ***: terminated Aborted (core dumped) Traceback: RuntimeError: subprocess exited with code 134. -- Amanda Rodrigue, PhD Boston Children's Hospital Harvard Medical School 1 Autumn St. Boston, MA 02215

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Requesting pass code for FS_7_2_0_ubuntu_18_04_06.ova.7z
by Yuxuan Liu 13 Nov '23

13 Nov '23

External Email - Use Caution I found there is a pass code required to unzip this file. Could someone send me this code? Thanks very much.

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Request for Passcode to Open 7z. Archive
by José Dixon 11 Nov '23

11 Nov '23

External Email - Use Caution Dear FreeSurfer Support Team, I need the passcode to extract the archive for VirtualBox Ubuntu 18.04.06 compressed image with FreeSurfer 7.2.0 (FS_7_2_0_Ubuntu_18_04_06.ova.7z). Thanks so much for fulfilling this request. -- Best, José Dixon Morgan State University | Ph.D. Student

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Importing atlas with mris_register: "hips not supported"
by Jasmine Cakmak 09 Nov '23

09 Nov '23

External Email - Use Caution Hello, Any help with this issue is greatly appreciated. I am trying to import the Neuromorphometrics atlas into Freesurfer as a part of my segmentation analysis. I have run recon-all on my template subject (IXI550) and the subject to register (PSCI15_003), and taken the atlas.nii and used mri_vol2surf and mris_seg2annot, all without errors. Now I am trying to register IXI550 and PSCI15_003 to each other so that I am then able to run mris_apply_reg. I am receiving the error "hips not supported," both on Ubuntu 22.04.2 LTS and my M1 mac. Is there a way to resolve this error (found below), or a different way for me to apply the atlas to the recon-all of my subjects? I am using freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275. mris_register PSCI15_003/surf/lh.sphere IXI550/surf/lh.sphere reg_PSCI15003_IXI550.dat cwd /mnt/d/Jasmine2023/Neuromorph cmdline mris_register PSCI15_003/surf/lh.sphere IXI550/surf/lh.sphere reg_PSCI15003_IXI550.dat 0 inflated.H 1 sulc 2 smoothwm (computed) 7.3.2 7.3.2 reading surface from PSCI15_003/surf/lh.sphere... reading template parameterization from IXI550/surf/lh.sphere... error: hips is not supported error: hips is not supported MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=unkno, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 -------------------- tol=5.0e-01, sigma=0.0, host=unkno, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization 1 Reading lh.sulc curvature mean = 0.000, std = 3.574 Segmentation fault Thank you so much in advance for any help. Jasmine

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Group analysis question
by Nicolette Barber 09 Nov '23

09 Nov '23

External Email - Use Caution Hello, I am working on a project using FreeSurfer, and I am trying to set up a whole brain group analysis. However, I am not sure how to set up the FSDG files, etc., as my dependent variable is not a cortical measurement. My dependent variable is a neuropsychological battery, culture, and brain measurement are my independent, and my covariate is ICV. I have been trying to figure this out for a while now. Is there a way to change the dependent variable for mriglm_fit? And if so, how would I set this up? I am using version 6. Thank you, Nicolette

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dt_recon question
by Mirsol Choi 09 Nov '23

09 Nov '23

External Email - Use Caution Hi there, I am currently going through the dt_recon tutorial on your website and I just have a quick question regarding the recon-all and dt_recon commands on freesurfer. For me to process dt_recon, my understanding is that I must process recon-all first. But where my confusion lies is: - do I perform recon-all on the actual dwi.nii.gz image, then dt_recon with the same dti files (including the bval and bvec of the same dwi.nii.gz file) OR - should I have two separate sets of data, one T1 and one DTI, and perform recon-all on T1 images and take DWI images from the same subject to perform dt_recon? My understanding was that the second bullet is the right way to go since the dt_recon uses the outputs from T1 recon-all to register properly. Please let me know which one is correct, and if I am missing something. Thank you so much for your help, I really appreciate your time. M

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SynthSEG continued developments
by Dawn Matthews 09 Nov '23

09 Nov '23

External Email - Use Caution Thank you for all of the work of the FreeSurfer team in continuing to make advances to the Freesurfer suite of tools. I wondered if you could comment on (a) any work or plans to include hippocampal subfield, brainstem subfield, or corpus callosum subfield segmentations, and (b) the robustness of SynthSEG to defacing/refacing software as compared to Freesurfer? Thanks very much.

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PETsurfer kinetic modeling
by Dawn Matthews 09 Nov '23

09 Nov '23

External Email - Use Caution Congratulations to the FreeSurfer team in the continued progress made in the FS tool set. I wondered if you could comment on whether it is feasible to create a custom reference region (other than specifying, for example, cerebellar cortex or another predefined FS mask) for PETsurfer kinetic modeling (e.g. a cerebellum subfield) or whether there perhaps is an existing cerebellar subfield atlas that can be run with PETSurfer (e.g. crus2)? In addition, can you please confirm whether the Logan model can be run using a reference region (i.e. without requiring arterial input)? Thanks very much and kind regards.

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Unsubscribe Mailing List
by yunus soleymani 09 Nov '23

09 Nov '23

External Email - Use Caution Hi Freesurfer Team Please unsubscribe my email from the list Email: soleymani.yunus(a)yahoo.comThanksYunus --------------------------------------------------------------------------------Yunus Soleymani Ph.D. Candidate of Neuroimaging Tehran University of Medical Sciences soleymani.yunus(a)yahoo.com+98 914 526 9298--------------------------------------------------------------------------------

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